The actor was arrested on Thursday by the city's cybercrime police for allegedly creating and uploading "objectionable" videos.
The content posted by Khan is "promoting enmity between different groups on grounds of religion, etc and creating hatred among the public at large", police had said after his arrest on Thursday.
The ex-Bigg Boss contestant's lawyer had earlier opposed the police custody on grounds that preliminary investigation was done before the arrest and also because the telecast material is already seized. The police, however, maintained that custody was required.
The police had received a complaint against him along with few videos which have gone viral on social media, said a press release.
'The case against the actor was registered under Indian Penal Code's Section 153A (promoting enmity between different groups on grounds of religion, race etc.) and Section 34 (Acts done by several persons in furtherance of common intention) along with Section 67 of the IT Act (publishing or transmitting obscene material in electronic form).
Further investigation is being carried out by Cyber Crime Police Station, Mumbai.
It is not for the first time that the actor has made headlines, last year he was arrested for possessing banned narcotic substance. He was arrested by Anti Narcotics Cell of the Mumbai police with eight ecstasy tablets.
The 39-year-old's past credits in Bollywood include, 'Allah Ke Banday', 'Singham Returns', 'Rakhta Charitra' and 'Bbuddah Hoga Terra Baap'. He was also seen in Salman Khan's reality show 'Bigg Boss 7'.
(Inputs added in ANI Copy)